Contacts of the helix formed by residues 1630 - 1645 (chain X) in PDB entry 3HM6
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER1630 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1627X ARG 5.8 0.4 - - - -
1628X THR 3.4 4.4 + - - -
1629X PHE* 1.3 72.8 - - - +
1631X ALA* 1.3 59.6 + - - +
1632X ARG* 3.6 9.7 + - - +
1633X ASP* 2.7 33.2 + - - -
1634X ARG* 2.9 35.4 + - - +
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Residues in contact with ALA1631 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1630X SER* 1.3 72.8 - - - +
1632X ARG* 1.3 66.4 + - - +
1634X ARG* 3.4 1.3 + - - +
1635X ALA* 3.0 26.0 + - - +
1679X THR 4.8 1.4 - - - +
1680X GLU* 3.6 52.1 - - + +
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Residues in contact with ARG1632 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17X UNX 3.3 22.2 - - - -
1580X HIS* 6.2 5.8 - - + -
1630X SER* 3.6 8.6 + - - +
1631X ALA* 1.3 78.4 - - - +
1633X ASP* 1.3 55.7 + - - +
1635X ALA* 3.8 4.8 - - - +
1636X TYR* 2.9 34.1 + - + +
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Residues in contact with ASP1633 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17X UNX 4.1 7.1 - - - -
1628X THR 3.3 12.3 - - - +
1629X PHE* 3.5 21.1 - - + -
1630X SER* 2.7 38.4 + - - +
1632X ARG* 1.3 76.6 - - - +
1634X ARG* 1.3 52.9 + - - +
1636X TYR* 3.2 2.3 + - - +
1637X VAL* 2.8 38.6 + - - +
2094X TYR* 2.7 36.4 + - - +
2097X LYS* 5.0 6.0 + - - -
2098X TYR* 4.8 0.9 + - - -
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Residues in contact with ARG1634 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1624X GLU* 2.9 64.1 + - - +
1626X GLN 3.6 9.9 + - - -
1627X ARG* 5.5 1.4 - - - +
1629X PHE* 2.9 50.6 + - + -
1630X SER 2.9 19.6 + - - +
1631X ALA* 3.8 1.1 - - - +
1632X ARG 3.4 0.2 - - - -
1633X ASP* 1.3 72.5 - - - +
1635X ALA* 1.3 57.9 + - - +
1637X VAL 3.9 0.2 - - - -
1638X ALA* 3.0 28.8 + - - +
1680X GLU 3.2 26.2 - - - +
1681X THR* 4.2 6.5 - - - +
1682X VAL* 3.5 20.4 - - + +
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Residues in contact with ALA1635 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1576X PHE 4.7 0.5 - - - +
1631X ALA 3.0 17.1 + - - +
1632X ARG* 3.9 4.7 - - - +
1634X ARG* 1.3 77.2 - - - +
1636X TYR* 1.3 61.8 + - - +
1639X SER* 3.3 20.4 + - - -
1679X THR* 4.4 14.6 - - + +
1680X GLU 4.6 0.6 + - - -
1681X THR 5.1 0.7 - - - -
1685X LYS* 3.3 38.8 - - + +
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Residues in contact with TYR1636 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17X UNX 4.5 5.4 - - - -
1576X PHE 5.7 0.7 - - - -
1577X PHE* 3.7 31.4 - + - -
1580X HIS* 4.6 12.1 - + - -
1584X PRO* 3.8 28.9 - - + +
1585X LEU* 4.3 0.7 - - - +
1632X ARG* 2.9 23.5 + - + +
1633X ASP* 3.7 2.7 - - - +
1635X ALA* 1.3 72.2 - - - +
1637X VAL* 1.3 61.7 + - - +
1639X SER* 3.2 4.9 + - - -
1640X LEU* 2.9 50.7 + - + +
2090X GLU* 2.7 39.3 + - - +
2094X TYR* 3.8 28.9 - + - -
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Residues in contact with VAL1637 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1619X PHE* 4.9 0.7 - - + -
1620X ILE* 5.9 1.3 - - + -
1623X LEU* 4.1 18.2 - - + -
1629X PHE* 3.6 25.4 - - + -
1633X ASP 2.8 22.5 + - - +
1634X ARG 4.0 2.5 - - - +
1636X TYR* 1.3 69.7 - - - +
1638X ALA* 1.3 63.9 + - - +
1640X LEU* 3.2 9.0 + - + +
1641X LEU* 2.9 37.6 + - + +
1682X VAL* 5.0 6.3 - - + -
2091X LEU* 3.8 17.7 - - + -
2094X TYR* 3.8 30.5 - - + -
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Residues in contact with ALA1638 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1634X ARG 3.0 17.7 + - - +
1635X ALA 3.6 0.2 - - - +
1637X VAL* 1.3 77.8 - - - +
1639X SER* 1.3 56.7 + - - +
1641X LEU* 3.5 1.4 + - - +
1642X THR* 2.9 30.8 + - - -
1682X VAL* 3.7 19.9 - - - +
1685X LYS* 3.5 32.3 - - + -
1686X LEU* 3.4 19.9 - - + +
1689X ASN* 4.2 0.7 - - - -
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Residues in contact with SER1639 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1576X PHE* 2.6 35.2 + - - -
1577X PHE* 3.5 19.5 - - - -
1635X ALA 3.3 4.0 + - - -
1636X TYR 3.2 5.6 + - - -
1638X ALA* 1.3 74.5 - - - +
1640X LEU* 1.3 66.3 + - - +
1642X THR* 3.4 1.4 + - - -
1643X VAL* 3.1 29.6 + - - +
1685X LYS* 3.3 9.2 - - - -
1689X ASN* 3.0 24.6 + - - +
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Residues in contact with LEU1640 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1577X PHE* 4.3 3.8 - - + -
1585X LEU* 3.8 24.0 - - + -
1636X TYR* 2.9 47.0 + - + +
1637X VAL* 3.6 10.5 - - - +
1639X SER* 1.3 77.6 - - - +
1641X LEU* 1.3 56.7 + - - +
1643X VAL* 3.6 0.6 + - - -
1644X ALA* 2.9 30.0 + - - +
2087X ALA* 3.7 16.8 - - + +
2090X GLU* 3.6 45.3 - - + +
2091X LEU* 3.7 24.0 - - + +
2094X TYR* 4.5 4.0 - - + -
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Residues in contact with LEU1641 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1610X LEU* 3.7 20.4 - - + -
1616X LEU* 3.7 25.8 - - + -
1619X PHE* 4.6 4.3 - - + -
1620X ILE* 4.1 27.8 - - + -
1637X VAL* 2.9 36.4 + - + +
1638X ALA* 3.6 8.1 - - - +
1640X LEU* 1.3 74.7 - - - +
1642X THR* 1.3 60.3 + - - +
1644X ALA* 3.3 2.5 + - - -
1645X LEU* 2.8 46.9 + - + +
1652X PHE* 4.8 0.4 - - + -
1682X VAL* 4.8 3.8 - - + -
1686X LEU* 4.6 7.4 - - + -
2091X LEU* 3.8 20.9 - - + -
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Residues in contact with THR1642 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1576X PHE* 3.4 35.2 - - + -
1638X ALA 2.9 19.4 + - - -
1639X SER 3.5 8.3 - - - -
1641X LEU* 1.3 75.9 - - - +
1643X VAL* 1.3 56.4 + - - +
1645X LEU 3.5 1.6 - - - -
1646X HIS* 3.0 31.6 + - + +
1649X LEU* 5.4 0.8 - - + +
1652X PHE* 3.6 27.6 - - + -
1686X LEU* 4.0 1.0 - - - +
1689X ASN* 3.1 19.2 + - + +
1693X ILE* 3.9 19.1 - - + -
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Residues in contact with VAL1643 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1576X PHE* 3.8 23.3 - - + -
1577X PHE* 4.3 4.7 - - + -
1585X LEU* 4.1 14.8 - - + -
1639X SER 3.1 16.7 + - - +
1640X LEU 3.9 3.8 - - - +
1642X THR* 1.3 78.2 - - - +
1644X ALA* 1.3 64.0 + - - +
1645X LEU 3.3 0.5 + - - -
1646X HIS* 3.4 17.5 + - - +
1647X GLY 5.1 0.3 + - - -
2082X LEU* 3.6 32.3 - - + +
2083X GLY 3.7 5.2 - - - +
2084X ALA* 3.6 35.7 - - + +
2087X ALA* 4.0 6.3 - - + -
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Residues in contact with ALA1644 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1607X SER* 4.8 8.7 + - - +
1610X LEU* 4.2 25.1 - - + -
1640X LEU 2.9 18.7 + - - +
1641X LEU* 3.7 4.5 - - - +
1643X VAL* 1.3 76.8 - - - +
1645X LEU* 1.3 63.6 + - + +
1646X HIS 3.8 0.5 + - - -
1647X GLY 4.9 1.9 + - - -
2084X ALA* 4.6 13.4 - - - +
2087X ALA* 4.6 2.9 - - + +
2088X LEU* 4.2 17.3 - - + -
2091X LEU* 4.3 5.2 - - + -
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Residues in contact with LEU1645 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1607X SER 5.6 0.4 - - - +
1610X LEU* 4.3 17.7 - - + -
1611X ASN* 4.0 13.9 - - - +
1616X LEU* 3.8 27.4 - - + -
1641X LEU* 2.8 31.3 + - + +
1642X THR 3.5 2.9 - - - +
1644X ALA* 1.3 82.1 - - + +
1646X HIS* 1.3 58.5 + - - +
1647X GLY 3.2 3.1 - - - -
1648X LYS* 3.0 33.9 + - + +
1649X LEU* 3.9 4.8 + - - +
1651X TYR* 4.0 26.2 - - + -
1652X PHE* 4.2 26.0 - - + +
1655X ILE* 5.3 1.6 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il